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Protein

Methyl-CpG-binding domain protein 2

Gene

MBD2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binds hemimethylated DNA as well. Recruits histone deacetylases and DNA methyltransferases. Acts as transcriptional repressor and plays a role in gene silencing. Functions as a scaffold protein, targeting GATAD2A and GATAD2B to chromatin to promote repression. May enhance the activation of some unmethylated cAMP-responsive promoters.6 Publications

GO - Molecular functioni

  • C2H2 zinc finger domain binding Source: UniProtKB
  • chromatin binding Source: Ensembl
  • methyl-CpG binding Source: UniProtKB
  • mRNA binding Source: Ensembl
  • protein domain specific binding Source: UniProtKB
  • satellite DNA binding Source: ProtInc
  • siRNA binding Source: Ensembl

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-73728. RNA Polymerase I Promoter Opening.

Names & Taxonomyi

Protein namesi
Recommended name:
Methyl-CpG-binding domain protein 2
Alternative name(s):
Demethylase
Short name:
DMTase
Methyl-CpG-binding protein MBD2
Gene namesi
Name:MBD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 18

Organism-specific databases

HGNCiHGNC:6917. MBD2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: Ensembl
  • heterochromatin Source: Ensembl
  • histone deacetylase complex Source: Ensembl
  • nuclear chromatin Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • protein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi8932.
OpenTargetsiENSG00000134046.
PharmGKBiPA30660.

Polymorphism and mutation databases

BioMutaiMBD2.
DMDMi50401198.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000962601 – 411Methyl-CpG-binding domain protein 2Add BLAST411

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei181PhosphoserineCombined sources1
Modified residuei407PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9UBB5.
MaxQBiQ9UBB5.
PaxDbiQ9UBB5.
PeptideAtlasiQ9UBB5.
PRIDEiQ9UBB5.

PTM databases

iPTMnetiQ9UBB5.
PhosphoSitePlusiQ9UBB5.

Expressioni

Tissue specificityi

Highly expressed in brain, heart, kidney, stomach, testis and placenta.1 Publication

Gene expression databases

BgeeiENSG00000134046.
CleanExiHS_MBD2.
ExpressionAtlasiQ9UBB5. baseline and differential.
GenevisibleiQ9UBB5. HS.

Organism-specific databases

HPAiCAB037282.
HPA067582.
HPA067615.

Interactioni

Subunit structurei

Heterodimer with MBD3. Component of the MeCP1 complex that contains HDAC1 and HDAC2. Binds DNMT1, MIZF, GPN1, SIN3A, GATAD2A/p66-alpha and GATAD2B/p66-beta. Interacts with DHX9.10 Publications

GO - Molecular functioni

  • C2H2 zinc finger domain binding Source: UniProtKB
  • protein domain specific binding Source: UniProtKB

Protein-protein interaction databases

BioGridi114445. 49 interactors.
IntActiQ9UBB5. 18 interactors.
MINTiMINT-210249.
STRINGi9606.ENSP00000256429.

Chemistry databases

BindingDBiQ9UBB5.

Structurei

Secondary structure

1411
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi366 – 388Combined sources23
Turni389 – 392Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L2LNMR-B360-393[»]
ProteinModelPortaliQ9UBB5.
SMRiQ9UBB5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini145 – 213MBDPROSITE-ProRule annotationAdd BLAST69

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 149Necessary for interaction with DHX91 PublicationAdd BLAST149

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi6 – 140Gly-richAdd BLAST135
Compositional biasi50 – 96Arg-richAdd BLAST47

Sequence similaritiesi

Contains 1 MBD (methyl-CpG-binding) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410INB9. Eukaryota.
ENOG410ZPAZ. LUCA.
GeneTreeiENSGT00410000025376.
HOGENOMiHOG000013073.
HOVERGENiHBG052417.
InParanoidiQ9UBB5.
KOiK11590.
OMAiNCISICC.
OrthoDBiEOG091G0I05.
PhylomeDBiQ9UBB5.
TreeFamiTF325032.

Family and domain databases

Gene3Di3.30.890.10. 2 hits.
InterProiIPR016177. DNA-bd_dom.
IPR032343. MBD2/MBD3_p55-bd.
IPR025884. MeCpG-bd_2/3_C_dom.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF14048. MBD_C. 1 hit.
PF16564. MBDa. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UBB5-1) [UniParc]FASTAAdd to basket
Also known as: MBD2a, MBD2b

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRAHPGGGRC CPEQEEGESA AGGSGAGGDS AIEQGGQGSA LAPSPVSGVR
60 70 80 90 100
REGARGGGRG RGRWKQAGRG GGVCGRGRGR GRGRGRGRGR GRGRGRPPSG
110 120 130 140 150
GSGLGGDGGG CGGGGSGGGG APRREPVPFP SGSAGPGPRG PRATESGKRM
160 170 180 190 200
DCPALPPGWK KEEVIRKSGL SAGKSDVYYF SPSGKKFRSK PQLARYLGNT
210 220 230 240 250
VDLSSFDFRT GKMMPSKLQK NKQRLRNDPL NQNKGKPDLN TTLPIRQTAS
260 270 280 290 300
IFKQPVTKVT NHPSNKVKSD PQRMNEQPRQ LFWEKRLQGL SASDVTEQII
310 320 330 340 350
KTMELPKGLQ GVGPGSNDET LLSAVASALH TSSAPITGQV SAAVEKNPAV
360 370 380 390 400
WLNTSQPLCK AFIVTDEDIR KQEERVQQVR KKLEEALMAD ILSRAADTEE
410
MDIEMDSGDE A
Length:411
Mass (Da):43,255
Last modified:May 1, 2000 - v1
Checksum:iFC4E5E0CF9BA0FFA
GO
Isoform 3 (identifier: Q9UBB5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     235-302: GKPDLNTTLP...SDVTEQIIKT → LRWNTHRPAP...YSRQNQSFPP
     303-411: Missing.

Note: Incomplete sequence.
Show »
Length:302
Mass (Da):31,745
Checksum:iCCEC65D926222717
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_011077235 – 302GKPDL…QIIKT → LRWNTHRPAPWHALSRLCLL IRCLLCLECAYPLPLHLVNS YSSKTQLHCLHLWEACPAYS RQNQSFPP in isoform 3. 1 PublicationAdd BLAST68
Alternative sequenceiVSP_011078303 – 411Missing in isoform 3. 1 PublicationAdd BLAST109

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072242 mRNA. Translation: AAC68871.1.
AF072246 mRNA. Translation: AAC68875.1.
AF120989, AF120988 Genomic DNA. Translation: AAD56596.1.
AF120993
, AF120988, AF120989, AF120990, AF120991, AF120992 Genomic DNA. Translation: AAD56597.1.
BC032638 mRNA. Translation: AAH32638.1.
CCDSiCCDS11953.1. [Q9UBB5-1]
CCDS45871.1. [Q9UBB5-3]
RefSeqiNP_003918.1. NM_003927.4. [Q9UBB5-1]
NP_056647.1. NM_015832.4. [Q9UBB5-3]
UniGeneiHs.25674.

Genome annotation databases

EnsembliENST00000256429; ENSP00000256429; ENSG00000134046. [Q9UBB5-1]
ENST00000583046; ENSP00000464554; ENSG00000134046. [Q9UBB5-3]
GeneIDi8932.
KEGGihsa:8932.
UCSCiuc002lfg.2. human. [Q9UBB5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF072242 mRNA. Translation: AAC68871.1.
AF072246 mRNA. Translation: AAC68875.1.
AF120989, AF120988 Genomic DNA. Translation: AAD56596.1.
AF120993
, AF120988, AF120989, AF120990, AF120991, AF120992 Genomic DNA. Translation: AAD56597.1.
BC032638 mRNA. Translation: AAH32638.1.
CCDSiCCDS11953.1. [Q9UBB5-1]
CCDS45871.1. [Q9UBB5-3]
RefSeqiNP_003918.1. NM_003927.4. [Q9UBB5-1]
NP_056647.1. NM_015832.4. [Q9UBB5-3]
UniGeneiHs.25674.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2L2LNMR-B360-393[»]
ProteinModelPortaliQ9UBB5.
SMRiQ9UBB5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114445. 49 interactors.
IntActiQ9UBB5. 18 interactors.
MINTiMINT-210249.
STRINGi9606.ENSP00000256429.

Chemistry databases

BindingDBiQ9UBB5.

PTM databases

iPTMnetiQ9UBB5.
PhosphoSitePlusiQ9UBB5.

Polymorphism and mutation databases

BioMutaiMBD2.
DMDMi50401198.

Proteomic databases

EPDiQ9UBB5.
MaxQBiQ9UBB5.
PaxDbiQ9UBB5.
PeptideAtlasiQ9UBB5.
PRIDEiQ9UBB5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000256429; ENSP00000256429; ENSG00000134046. [Q9UBB5-1]
ENST00000583046; ENSP00000464554; ENSG00000134046. [Q9UBB5-3]
GeneIDi8932.
KEGGihsa:8932.
UCSCiuc002lfg.2. human. [Q9UBB5-1]

Organism-specific databases

CTDi8932.
DisGeNETi8932.
GeneCardsiMBD2.
HGNCiHGNC:6917. MBD2.
HPAiCAB037282.
HPA067582.
HPA067615.
MIMi603547. gene.
neXtProtiNX_Q9UBB5.
OpenTargetsiENSG00000134046.
PharmGKBiPA30660.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410INB9. Eukaryota.
ENOG410ZPAZ. LUCA.
GeneTreeiENSGT00410000025376.
HOGENOMiHOG000013073.
HOVERGENiHBG052417.
InParanoidiQ9UBB5.
KOiK11590.
OMAiNCISICC.
OrthoDBiEOG091G0I05.
PhylomeDBiQ9UBB5.
TreeFamiTF325032.

Enzyme and pathway databases

ReactomeiR-HSA-427413. NoRC negatively regulates rRNA expression.
R-HSA-73728. RNA Polymerase I Promoter Opening.

Miscellaneous databases

ChiTaRSiMBD2. human.
GeneWikiiMethyl-CpG-binding_domain_protein_2.
GenomeRNAii8932.
PROiQ9UBB5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000134046.
CleanExiHS_MBD2.
ExpressionAtlasiQ9UBB5. baseline and differential.
GenevisibleiQ9UBB5. HS.

Family and domain databases

Gene3Di3.30.890.10. 2 hits.
InterProiIPR016177. DNA-bd_dom.
IPR032343. MBD2/MBD3_p55-bd.
IPR025884. MeCpG-bd_2/3_C_dom.
IPR001739. Methyl_CpG_DNA-bd.
[Graphical view]
PfamiPF01429. MBD. 1 hit.
PF14048. MBD_C. 1 hit.
PF16564. MBDa. 1 hit.
[Graphical view]
SMARTiSM00391. MBD. 1 hit.
[Graphical view]
SUPFAMiSSF54171. SSF54171. 1 hit.
PROSITEiPS50982. MBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMBD2_HUMAN
AccessioniPrimary (citable) accession number: Q9UBB5
Secondary accession number(s): O95242, Q9UIS8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: May 1, 2000
Last modified: November 30, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

Functional studies (PubMed:10050851, PubMed:10950960 and PubMed:12665568) have used a C-terminal fragment of isoform 1 which has been described originally as isoform MBD2b but cannot however be proven by supporting cDNA sequences.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 18
    Human chromosome 18: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.